Closed creisle closed 3 years ago
Merging #235 (e7127e7) into master (74cc132) will increase coverage by
10.64%
. The diff coverage is78.26%
.
@@ Coverage Diff @@
## master #235 +/- ##
===========================================
+ Coverage 80.51% 91.16% +10.64%
===========================================
Files 52 52
Lines 9126 9132 +6
===========================================
+ Hits 7348 8325 +977
+ Misses 1778 807 -971
Flag | Coverage Δ | |
---|---|---|
unittests | 91.16% <78.26%> (+10.64%) |
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Impacted Files | Coverage Δ | |
---|---|---|
mavis/schedule/local.py | 73.46% <66.66%> (+47.93%) |
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mavis/schedule/pipeline.py | 73.31% <90.90%> (+17.62%) |
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mavis/annotate/fusion.py | 96.02% <0.00%> (+0.33%) |
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mavis/bam/cigar.py | 98.14% <0.00%> (+0.61%) |
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mavis/bam/cache.py | 88.31% <0.00%> (+0.64%) |
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mavis/schedule/job.py | 78.26% <0.00%> (+0.72%) |
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mavis/cluster/main.py | 90.24% <0.00%> (+0.81%) |
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mavis/annotate/genomic.py | 93.12% <0.00%> (+1.03%) |
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mavis/breakpoint.py | 95.00% <0.00%> (+1.53%) |
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mavis/illustrate/elements.py | 96.37% <0.00%> (+1.69%) |
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... and 18 more |
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The error fix will now report this error
'The mavis executable was not found on the current PATH. '
FileNotFoundError: The mavis executable was not found on the current PATH. This is required in order to run external scripts. Please add mavis to the PATH with PATH=$PATH:/path/to/mavis/bin
Instead of the less informative
File "...pipeline.py", line 277, in write_submission_script
fh.write(' \\\n\t'.join(commands) + '\n\n')
TypeError: sequence item 0: expected str instance, NoneType found
BugFixes
Improvements
234 add better error message for mavis not found on path